This next bit of pondering is merely fanciful thought, but what if the Forerunner believed that genetic perfection was most important above all else. They would be the organic equivalent to Star Trek's BORG. They searched the galaxy looking for genetic material with which they could further their quest for perfection. The Flood just happened to be one of these. After they had introduced the plus parts of the Flood or any other genetic material into their own matrices they would cleanse or "Reclaim" the space that material inhabited so that only they (The Forerunner) with their perfect selves would exist. This still doesn't answer what happened to the Forerunner, who knows maybe they died out because of lack of new genetic difference (inbreeding is bad).

So were the Flood encountered and used in this quest for genetic supremacy, or were they created as a product of it? Would they be an attempt at, or a stepping stone to, the perfect organism?